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HOSPITAL. Sherlock is lying barely conscious in bed, a nasal cannula on his face. His room is filled with vases of flowers. Magnussen walks to the door, opens it and comes in. Sherlock’s eyes roll sideways and he fuzzily sees the man standing in the doorway. MAGNUSSEN: They’re not all from me.(Sherlock turns his head slightly towards him as he closes the door. Magnussen points to one of the vases on the bureau.)MAGNUSSEN: The struggling carnations are from Scotland Yard.(He looks across to a rose on its own in another vase at the end of Sherlock’s bed.)MAGNUSSEN: And the single rose is from ...(He walks closer and looks at the card propped up against the vase.)MAGNUSSEN: ... ‘W’.(He sounds intrigued as he looks at the large letter ‘W’ on the card.)MAGNUSSEN (pointing to more flowers on the other side of the bed): And the black wreath – C Block, Pentonville. I’m not sure the intent was entirely kindly.(He sits on the chair to the right of Sherlock’s bedside. Looking down, he puts his left hand on Sherlock’s forearm and runs his right hand up and down the back of Sherlock’s hand.)MAGNUSSEN: Oh, I covet your hands, Mr Holmes; though since you’ve survived, I suppose you get to keep them.(He moves his left hand to Sherlock’s wrist and lifts it a few inches off the bed.)MAGNUSSEN: Look at them.(He takes the pulse oximeter from Sherlock’s finger and puts it onto the bed, then puts the backs of his own fingers under Sherlock’s before running his fingertips over the top.)MAGNUSSEN: The musician’s hands.(He moves his hand down to gently hold the end of Sherlock’s fingers.)MAGNUSSEN: An artist’s.(He leans forward, opens his mouth slightly and presses it against the back of Sherlock’s hand. After a moment he lifts his head and looks at Sherlock, whose breathing deepens a little while he looks back at the fuzzy image of the man.)MAGNUSSEN: Or a woman’s?(Sherlock manages to pull his hand free. Magnussen lets it go and it flops onto the bed. Magnussen rubs his own hands together.)MAGNUSSEN: Apologies for the dampness of my touch.(He sits back a little, still looking at Sherlock’s face.)MAGNUSSEN: You’ll get used to it.(Sherlock continues to breathe deeply.)MAGNUSSEN: Having shot you, the woman you know as Mary Watson left without killing me.(He picks up the pulse oximeter and clips it back onto Sherlock’s middle finger.)MAGNUSSEN: ... which is odd, because that was the reason she came.(He stands up, steps closer to the top of the bed and slowly bends down, bringing his mouth very close to Sherlock’s face. Sherlock’s breathing deepens even more.)MAGNUSSEN (softly): I didn’t pass on her identity to the police. Information like that is just too ...(He runs his nose over the end of Sherlock’s. Again Sherlock’s breathing sharpens.)MAGNUSSEN: ... malleable to be shared.(Sherlock stares up at him, his pupils almost pinpricks.)MAGNUSSEN: Wouldn’t you agree?(Sherlock’s eyes flicker and begin to close. Magnussen straightens up and leaves the room. Sherlock’s eyes open a little for a moment, and then close.)

A full list of episode transcripts, DVD commentary summaries/transcripts, and transcripts of the DVD special features can be found here.

Hmm, I've listened to it several more times and I still think it's 'malleable'. I think he means it in the context that he can use the information (about Mary) in any way he sees fit, bending it to his own purposes.

Wow, that was fast! Thank you so much for your invaluable transcripts. I found some words harder to understand than usual and actually wondered if the outstanding mumbling qualities of this scene were one of the reasons to delete it. On the other hand it might just be my complete lack of knowledge about flower names in English. ;) Anyway, thanks for your outstanding service to the fandom!

Thank you thank you as always for these incredible transcripts! But damn, this scene is so creepy! To me, it's how Magnussen doesn't really kiss Sherlock's hand, he kind of licks/sucks on it and Sherlock's helpless to get away. Poor Sherlock!

I finally got to see the video of this... someone posted a link on Tumblr... and this is what I said about it...

Ya know what… I think it’s a good thing they deleted that scene. I’m sure plenty of people will probably disagree with me, but I really think that was just way, WAY, WAY too creepy. There’s obviously a certain level of creepiness about Magnussen that was artistically necessary in order to properly tell this story, but that… that was just way too much. That’s like a stomach-turning, pukey, not-really-appropriate kinda creepiness that just disturbed the entire feel of the story. And besides, I think speculating about the rose rather than knowing exactly who it came from was much more intriguing.

And then later, I said:

I still think deleting this scene was the right move. Looking at it closely, this was essentially as literal of an allegory of a rape scene as probably was allowed to be broadcast on BBC One… notice the intimate manner in which Magnussen is touching Sherlock’s hands, referring to them as a woman’s, kissing Sherlock’s hand, telling Sherlock he’ll get used to his damp touch, and then in the last black and white gif, their noses are just about touching, and Magnussen’s mouth is literally an inch away from Sherlock’s. Magnussen physically violated his victims all throughout the episode, but this was a violation on a whole other level of wrong. So despite the inherent creepiness of Magnussen and the story line about him, the point was well gotten without the scene. I think it was too much.

And even aside from that, it splits the reason for Sherlock killing Magnussen at the end. Without the scene, Sherlock’s reason is all about his relationship with John (regardless of how you “orientate” it), knowing that what just happened was his fault, and him choosing to sacrifice his life to save John’s and Mary’s. With the scene, there’s now a secondary reason of Magnussen basically sexually assaulting him looming in the background, which throws in an element of self that takes away a lot of the weight carried by the first reason. Honestly, I think the story is better without it because Sherlock’s reason in the end is now completely selfless, and it’s a heavier, more inherently and relatably human example of unconditional love that way, and it just hits you in the feels like a cement slab.

Especially with the point in your last paragraph. I didn't know about this scene until now, and "His Last Vow" has always been all about self-sacrifice. He'll do anything to protect John and Mary, and all the other people Magnussen destroys. He hates Magnussen, that's obvious, but it's not because of anything Magnussen has done to him personally.

Magnussen's behavior may seem a sexual abuse, but actually it's a blackmail, that's all. He knew some facts about Sherlock that could "blow up" England.He did have reason to call Sherlock a woman (he is XXY apparently). He did have reason to take notice of Sherlock's hands. A glove tree in Magnussen's mind palace,remember? Cutting this scene deprived us of important evidence though it's very creepy indeed.

Assuming that Sherlock did have Klinefelter's Syndrome (karyotype XXY, caused by meiotic nondisjunction - that is, improper separation of the chromosomes during the formation of the egg or sperm cells), he would still be classified as genetically male since he has a Y chromosome. The only physical traits found in Klinefelter patients that might apply to Sherlock are that he is tall and slender, has a youthful facial appearance relative to his age, and doesn't have much/any hair on his chest - but the first two are also fairly common traits in the general (non-Klinefelter) population, and his lack of chest hair may be a cosmetic choice or an innocuous genetic trait. More importantly, Sherlock lacks other, more typical Klinefelter's symptoms such as wide hips coupled with a short torso and a femininely-curvy backside, gynecomastia (enlarged breast tissue), muscular weakness and lack of muscular definition, low energy and reduced physical stamina, and most especially, diminished executive and/or cognitive functionalities (language acquisition and usage, memory problems, and difficulty with decision-making and problem-solving).

I doubt that Magnussen's actions in the hospital room were an attempt at blackmailing Sherlock for "being a woman;" I think he was just pulling the same trick we saw him use in Lady Smallwood's office and during the meeting with John and Sherlock at Baker Street. That is, Magnussen was intentionally violating another individual's "personal space" by ignoring social norms about interpersonal proximity and by initiating inappropriate physical contact, thereby using those tactics to send the psychological message that he (Magnussen) is the dominant and more powerful party of the two, and that he doesn't give a lick about what's considered socially proper or morally right. That is also why he used Sherlock's fireplace as a urinal during their first encounter and later why he was picking through the remains of Sherlock's lunch and using his water glass as a finger bowl. It's all about Magnussen asserting his power and trying to establish himself as having the dominant position.

Thanks so much for posting this! I hope you don't mind I friended you--I just got into BBC Sherlock in the last year or so. Was this deleted scene put on that new Three Season Box Set that recently was released? thanks again!